Target found for triple negative breast cancer

Graphic representation of cancer cells.

College of Natural Resources researchers have found a long-elusive Achilles’ heel within “triple-negative” breast tumors, a common type of breast cancer that is difficult to treat. Such cancers account for about one in five instances of the disease, and they are deadlier than other forms of breast cancer, in part because no drugs have been developed to specifically target their tumors.

“We were looking for targets that drive cancer metabolism in triple-negative breast cancer, and we found one that was very specific to this type of cancer,” said Daniel K. Nomura, an associate professor of nutritional sciences and toxicology (NST) and of chemistry. Nomura was the senior author for the study, which was published in Cell Chemical Biology last spring.

Tumor cells develop an abnormal metabolism, which they rely on to get the energy boost they need to fuel their rapid growth. In its study, Nomura’s research team used an innovative approach to search for active enzymes that triple-negative breast cancers use differently for metabolism than other cells and even other tumors.

The team discovered that triple-negative breast cancer cells rely on vigorous activity by an enzyme called glutathione-S-transferase Pi1. The scientists then used a drug-like molecule named LAS17 to successfully target this vulnerability, killing cancer cells in the lab and shrinking tumors in mice.

The team intends to continue studying LAS17, Nomura said, the next step being to study tumor tissue resected from human triple-negative breast cancers and transplanted directly into mice.

The study’s authors also included NST’s Sharon Louie, Elizabeth Grossman, Lucky Ding, Tucker Huffman, and David Miyamoto; Roman Camarda and Andrei Goga of UC San Francisco; and Eranthie Weerapana and Lisa Crawford of Boston College.

— Adapted from an article by Jeffrey Norris

The Secret Language of Microbes

The fungus Neurospora crassa colonizing a burned tree (left) and a microscopic view of the fusion of germlings.

Images courtesy of N. Louise Glass.

Fungi communicate only via chemical signals, but, like humans, they appear to use different dialects. This discovery came from a Berkeley study of the filamentous fungus Neurospora crassa, a red bread mold that has been observed in the laboratory for nearly 100 years. The paper was published last spring in PLOS Biology.

Many fungi, including N. crassa, grow as filaments or hyphae that often fuse to form an interconnected network. Hyphal networks have been shown to be important to many fungi, including the mycorrhizal fungi that form associations with plant roots, sharing nutrients.

The study’s senior author, N. Louise Glass, a professor in the Department of Plant and Microbial Biology, said that the finding could help scientists understand how fungi communicate and cooperate for destructive purposes, such as plant diseases and animal mycoses, as well as beneficial purposes, such as symbiotic associations with plants.

“Our findings reveal a heretofore underappreciated complexity in fungal communication,” said Glass. “We have only scratched the surface on the communication and interactions of these enigmatic organisms.”

— Adapted from an article by Robert Sanders

Reconnecting people with native food

In most Native American communities around the country, residents are more than twice as likely as the general population to suffer from type 2 diabetes. The Native people in the Klamath Basin, a river basin that runs from Southern Oregon into the northern part of California, are no exception—they suffer from a range of diet-related illnesses. In some parts of the region, the nearest grocery store is a two-hour drive away, qualifying these areas as “food deserts.”

Today, the Klamath Basin is home to nearly 10,000 Native Americans, including members of the Karuk, Yurok, and Klamath Tribes. But the foods and food-related traditions of their ancestors have almost disappeared. These tribes once subsisted sustainably on the fertile land adjacent to the Klamath River. They fished for salmon, hunted for elk and deer, and gathered nuts and berries. Colonization gradually changed all that, with mining, logging, and dams that degraded the natural environment.

Now, the Klamath Basin Tribal Food Security Project is trying to ensure that these native foods are restored for younger generations. Jennifer Sowerwine (a cooperative extension specialist in the Department of Environmental Science, Policy, and Management) and her husband, Tom Carlson (a professor in the Department of Integrative Biology) are working with other Berkeley faculty and graduate students, as well as leaders in the Klamath Basin tribal communities, to identify the major barriers to producing native foods in the region. Currently in its fourth year of a five-year, $4 million grant from the U.S. Department of Agriculture, the group is seeing real results.

So far, more than 4,000 people have taken part in community garden workshops, surveys, focus groups, policy discussions, food production workshops, native-food camps, and after-school programs. In one year alone, nearly 400 workshops were held that brought together tribal elders with subsistence skills and tribal youths interested in learning how to butcher, can, bake, and ferment. A K–12 program is in the works.

There has been “a really strong retention of knowledge and wisdom around landscape management” among elders, said Sowerwine, especially when it comes to such practices as harvesting food, prescribed forest burns, and basketry.

— Adapted from an article by Alix Wall, originally published on civileats.com

Wealth of unexpected new microbes expands tree of life

An artistic representation of the tree of life, with many new groups of bacteria on the left, the uncultivable bacteria at upper right (purple), and the archaea and eukaryotes (green)—including humans—at lower right.

Illustration by Zosia Rostomian.

Imagine that you suddenly discovered 1,000 new ancestors or relatives in your family tree. That’s essentially what’s happened to the “tree of life,” a system of illustrating how earthly life has evolved and diversified.

Over the past 15 years, UC Berkeley researchers have discovered more than 1,000 new types of bacteria and archaea lurking in Earth’s nooks and crannies. Now, the tree has been dramatically restructured to account for these newly known microscopic life-forms.

The revised tree, published online in April in the new journal Nature Microbiology, reinforces once again that the life we see around us—plants, animals, humans, and other so-called eukaryotes—represents a tiny percentage of the world’s biodiversity.

“The tree of life is one of the most important organizing principles in biology,” said Jill Banfield—a UC Berkeley professor of earth and planetary science and of environmental science, policy, and management, and one of the article’s co-authors.

Much of this microbial diversity remained hidden until the genome revolution allowed researchers like Banfield to search directly for genomes in the environment, rather than trying to culture microbes in a lab dish. Many of the microbes can’t be isolated and cultured, because they’re not able to live on their own: They must beg, borrow, or steal stuff from other animals or microbes, as either parasites, symbiotic organisms, or scavengers.

“The new depiction will be of use not only to biologists who study microbial ecology,” said Banfield, “but also to biochemists searching for novel genes and researchers studying evolution and earth history.”

— Adapted from a story by Robert Sanders

A Tiny House in Berkeley's Back Yard

The THIMBY student team takes a break from constructing its tiny house in July 2016. From Left: Kenny Gotlieb, Ian Bolliger, AJ Glassman, Sabrina Werts, Laney Siegner, and Oriya Cohen.

Photo by AJ Glassman.

When about 190 nations attended the 2015 United Nations Climate Change Conference (known as COP21) in Paris last winter, more than half a million activists marched in cities around the world. At the summit itself, three UC Berkeley students presented a project at the Global University Climate Forum, sponsored by the International Alliance of Research Universities. Leading the contingent was Ian Bolliger, a PhD student in the Energy and Resources Group (ERG).

The students’ project, called Tiny House in My Back Yard (THIMBY), is an off-grid micro-house, which they’re designing and building with sponsorship from ERG and campus student-supported groups like the Green Initiative Fund. THIMBY addresses two issues: affordable, sustainable housing and carbon emissions. “Consensus on a global scale can never be sufficiently ambitious,” Bolliger said. “We need to take a bottom-up approach, with our own boots on the ground.”

Bolliger and an interdisciplinary team of both undergraduate and graduate students from more than 12 Berkeley departments are working on the house’s construction at the Richmond Field Station. They plan to have the structure completed by October 2016, to compete in the Sacramento Municipal Utility District’s 2016 Tiny House Competition.

The 170-square-foot, 100 percent solar-powered home on wheels will feature such cutting-edge energy- and water-efficiency systems as a living wall to filter household gray water and a composting toilet and solid waste “oven” to allow for composting of human waste. A lithium-ion battery will store energy from eight solar panels, and an air-to-water heat pump will provide hot water and space heating through a hydronic radiant floor system.

In collaboration with the Bay Area Environmentally Aware Consulting Network, the team has developed a tool to quantify the house’s embedded carbon emissions, which it estimates to be around 18 metric tons of carbon dioxide equivalent (tCO2e). A typical 1,750-square-foot house has around 80 tCO2e of embedded emissions, plus additional yearly emissions associated with natural gas and grid electricity use. Finally, THIMBY will be small enough to fit in the back yards of most urban lots.